NextSeq_PanHaemOnc_2022_32: Quality control summary

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        Note that additional data was saved in /mnt/data/sequencers/220527_NDX550300_RUO_0152_AH3J33BGXM/NextSeq_PanHaemOnc_2022_32/reports/NextSeq_PanHaemOnc_2022_32_multiqc_report_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.8 (4c6300c)

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        NextSeq_PanHaemOnc_2022_32: Quality control summary

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Application Type
        DNA-seq
        Contact email
        helena.spiewak@nhs.net
        Panel
        PanHaemOnc
        Genome
        hg19
        Pipeline version
        3.5.0 (2021-04-16)

        Report generated on 2022-05-30, 13:37 based on data in:

        General Statistics

        Showing 441/441 rows and 10/13 columns.
        Sample NameM Reads MappedFold EnrichmentTarget Bases 10XTarget Bases 50XTarget Bases 100XInsert Size% Dups% Dups% GCM Seqs
        H10334-22
        19.3
        754
        99%
        98%
        97%
        189 bp
        10.2%
        H10334-22_S2_L001_R1_001
        15.0%
        47%
        2.8
        H10334-22_S2_L001_R2_001
        14.7%
        47%
        2.8
        H10334-22_S2_L002_R1_001
        15.0%
        47%
        2.8
        H10334-22_S2_L002_R2_001
        14.6%
        47%
        2.8
        H10334-22_S2_L003_R1_001
        15.2%
        47%
        2.8
        H10334-22_S2_L003_R2_001
        15.0%
        47%
        2.8
        H10334-22_S2_L004_R1_001
        15.0%
        47%
        2.8
        H10334-22_S2_L004_R2_001
        14.6%
        47%
        2.8
        H11184-22
        16.3
        785
        98%
        97%
        96%
        187 bp
        9.2%
        H11184-22_S3_L001_R1_001
        13.6%
        47%
        2.3
        H11184-22_S3_L001_R2_001
        13.3%
        47%
        2.3
        H11184-22_S3_L002_R1_001
        13.8%
        47%
        2.3
        H11184-22_S3_L002_R2_001
        13.1%
        47%
        2.3
        H11184-22_S3_L003_R1_001
        13.8%
        47%
        2.4
        H11184-22_S3_L003_R2_001
        13.3%
        47%
        2.4
        H11184-22_S3_L004_R1_001
        13.6%
        47%
        2.3
        H11184-22_S3_L004_R2_001
        13.1%
        47%
        2.3
        H13025-22
        17.9
        869
        98%
        97%
        97%
        149 bp
        10.8%
        H13025-22_S47_L001_R1_001
        15.7%
        48%
        2.6
        H13025-22_S47_L001_R2_001
        15.1%
        48%
        2.6
        H13025-22_S47_L002_R1_001
        15.7%
        48%
        2.6
        H13025-22_S47_L002_R2_001
        15.2%
        48%
        2.6
        H13025-22_S47_L003_R1_001
        15.8%
        48%
        2.7
        H13025-22_S47_L003_R2_001
        15.4%
        48%
        2.7
        H13025-22_S47_L004_R1_001
        15.6%
        48%
        2.6
        H13025-22_S47_L004_R2_001
        15.1%
        48%
        2.6
        H13110-22
        16.0
        881
        98%
        97%
        96%
        142 bp
        9.7%
        H13110-22_S4_L001_R1_001
        14.3%
        47%
        2.3
        H13110-22_S4_L001_R2_001
        14.2%
        48%
        2.3
        H13110-22_S4_L002_R1_001
        14.2%
        47%
        2.3
        H13110-22_S4_L002_R2_001
        13.9%
        48%
        2.3
        H13110-22_S4_L003_R1_001
        14.7%
        47%
        2.4
        H13110-22_S4_L003_R2_001
        14.2%
        48%
        2.4
        H13110-22_S4_L004_R1_001
        14.4%
        47%
        2.3
        H13110-22_S4_L004_R2_001
        14.0%
        48%
        2.3
        H13191-22
        14.6
        875
        99%
        98%
        96%
        142 bp
        9.3%
        H13191-22_S5_L001_R1_001
        13.4%
        48%
        2.1
        H13191-22_S5_L001_R2_001
        13.1%
        48%
        2.1
        H13191-22_S5_L002_R1_001
        13.4%
        48%
        2.1
        H13191-22_S5_L002_R2_001
        13.0%
        48%
        2.1
        H13191-22_S5_L003_R1_001
        13.6%
        48%
        2.1
        H13191-22_S5_L003_R2_001
        13.1%
        48%
        2.1
        H13191-22_S5_L004_R1_001
        13.4%
        48%
        2.1
        H13191-22_S5_L004_R2_001
        12.9%
        48%
        2.1
        H13741-22
        18.9
        771
        99%
        98%
        97%
        189 bp
        9.8%
        H13741-22_S6_L001_R1_001
        15.4%
        47%
        2.7
        H13741-22_S6_L001_R2_001
        14.9%
        47%
        2.7
        H13741-22_S6_L002_R1_001
        15.3%
        47%
        2.7
        H13741-22_S6_L002_R2_001
        14.7%
        47%
        2.7
        H13741-22_S6_L003_R1_001
        15.3%
        47%
        2.8
        H13741-22_S6_L003_R2_001
        15.0%
        47%
        2.8
        H13741-22_S6_L004_R1_001
        15.2%
        47%
        2.7
        H13741-22_S6_L004_R2_001
        14.8%
        47%
        2.7
        H13764-22
        18.8
        774
        98%
        97%
        97%
        188 bp
        10.0%
        H13764-22_S7_L001_R1_001
        14.9%
        47%
        2.7
        H13764-22_S7_L001_R2_001
        14.7%
        47%
        2.7
        H13764-22_S7_L002_R1_001
        14.9%
        47%
        2.7
        H13764-22_S7_L002_R2_001
        14.6%
        47%
        2.7
        H13764-22_S7_L003_R1_001
        14.9%
        47%
        2.8
        H13764-22_S7_L003_R2_001
        14.6%
        47%
        2.8
        H13764-22_S7_L004_R1_001
        14.9%
        47%
        2.7
        H13764-22_S7_L004_R2_001
        14.5%
        47%
        2.7
        H13876-22
        18.2
        778
        99%
        98%
        97%
        187 bp
        9.4%
        H13876-22_S8_L001_R1_001
        14.7%
        48%
        2.6
        H13876-22_S8_L001_R2_001
        14.0%
        48%
        2.6
        H13876-22_S8_L002_R1_001
        14.5%
        48%
        2.6
        H13876-22_S8_L002_R2_001
        13.7%
        48%
        2.6
        H13876-22_S8_L003_R1_001
        14.7%
        47%
        2.7
        H13876-22_S8_L003_R2_001
        13.8%
        48%
        2.7
        H13876-22_S8_L004_R1_001
        14.6%
        47%
        2.6
        H13876-22_S8_L004_R2_001
        13.8%
        48%
        2.6
        H14091-22
        18.8
        762
        98%
        98%
        97%
        185 bp
        9.2%
        H14091-22_S9_L001_R1_001
        14.5%
        47%
        2.7
        H14091-22_S9_L001_R2_001
        13.4%
        47%
        2.7
        H14091-22_S9_L002_R1_001
        14.4%
        47%
        2.7
        H14091-22_S9_L002_R2_001
        13.3%
        47%
        2.7
        H14091-22_S9_L003_R1_001
        14.5%
        47%
        2.8
        H14091-22_S9_L003_R2_001
        13.2%
        47%
        2.8
        H14091-22_S9_L004_R1_001
        14.4%
        47%
        2.7
        H14091-22_S9_L004_R2_001
        13.1%
        47%
        2.7
        H14210-22
        18.6
        765
        99%
        98%
        97%
        184 bp
        9.4%
        H14210-22_S10_L001_R1_001
        14.6%
        47%
        2.7
        H14210-22_S10_L001_R2_001
        14.2%
        47%
        2.7
        H14210-22_S10_L002_R1_001
        14.5%
        47%
        2.7
        H14210-22_S10_L002_R2_001
        14.1%
        47%
        2.7
        H14210-22_S10_L003_R1_001
        14.8%
        47%
        2.7
        H14210-22_S10_L003_R2_001
        14.5%
        47%
        2.7
        H14210-22_S10_L004_R1_001
        14.4%
        47%
        2.7
        H14210-22_S10_L004_R2_001
        14.1%
        47%
        2.7
        H14328-22
        18.6
        760
        98%
        97%
        97%
        190 bp
        9.2%
        H14328-22_S11_L001_R1_001
        14.2%
        47%
        2.6
        H14328-22_S11_L001_R2_001
        13.9%
        48%
        2.6
        H14328-22_S11_L002_R1_001
        14.1%
        47%
        2.6
        H14328-22_S11_L002_R2_001
        14.0%
        48%
        2.6
        H14328-22_S11_L003_R1_001
        14.3%
        47%
        2.7
        H14328-22_S11_L003_R2_001
        14.0%
        48%
        2.7
        H14328-22_S11_L004_R1_001
        14.1%
        47%
        2.6
        H14328-22_S11_L004_R2_001
        13.9%
        48%
        2.6
        H14329-22
        17.1
        748
        99%
        98%
        96%
        189 bp
        9.5%
        H14329-22_S12_L001_R1_001
        13.5%
        47%
        2.5
        H14329-22_S12_L001_R2_001
        12.9%
        47%
        2.5
        H14329-22_S12_L002_R1_001
        13.4%
        47%
        2.5
        H14329-22_S12_L002_R2_001
        12.8%
        47%
        2.5
        H14329-22_S12_L003_R1_001
        13.6%
        47%
        2.5
        H14329-22_S12_L003_R2_001
        13.0%
        47%
        2.5
        H14329-22_S12_L004_R1_001
        13.5%
        47%
        2.5
        H14329-22_S12_L004_R2_001
        13.0%
        47%
        2.5
        H14341-22
        15.5
        769
        99%
        98%
        96%
        184 bp
        9.1%
        H14341-22_S13_L001_R1_001
        12.5%
        47%
        2.2
        H14341-22_S13_L001_R2_001
        12.1%
        47%
        2.2
        H14341-22_S13_L002_R1_001
        12.6%
        47%
        2.2
        H14341-22_S13_L002_R2_001
        12.2%
        47%
        2.2
        H14341-22_S13_L003_R1_001
        12.4%
        47%
        2.3
        H14341-22_S13_L003_R2_001
        12.2%
        47%
        2.3
        H14341-22_S13_L004_R1_001
        12.7%
        47%
        2.2
        H14341-22_S13_L004_R2_001
        12.2%
        47%
        2.2
        H14462-22
        16.5
        761
        99%
        98%
        96%
        186 bp
        9.5%
        H14462-22_S14_L001_R1_001
        13.5%
        47%
        2.4
        H14462-22_S14_L001_R2_001
        13.0%
        47%
        2.4
        H14462-22_S14_L002_R1_001
        13.4%
        47%
        2.4
        H14462-22_S14_L002_R2_001
        13.0%
        47%
        2.4
        H14462-22_S14_L003_R1_001
        13.5%
        47%
        2.4
        H14462-22_S14_L003_R2_001
        12.9%
        47%
        2.4
        H14462-22_S14_L004_R1_001
        13.4%
        47%
        2.4
        H14462-22_S14_L004_R2_001
        12.9%
        47%
        2.4
        H14466-22
        16.5
        744
        99%
        98%
        96%
        190 bp
        9.8%
        H14466-22_S15_L001_R1_001
        13.1%
        47%
        2.4
        H14466-22_S15_L001_R2_001
        12.9%
        47%
        2.4
        H14466-22_S15_L002_R1_001
        13.0%
        47%
        2.4
        H14466-22_S15_L002_R2_001
        13.0%
        47%
        2.4
        H14466-22_S15_L003_R1_001
        13.2%
        47%
        2.4
        H14466-22_S15_L003_R2_001
        13.0%
        47%
        2.4
        H14466-22_S15_L004_R1_001
        13.1%
        47%
        2.4
        H14466-22_S15_L004_R2_001
        12.9%
        47%
        2.4
        H14473-22
        18.4
        772
        99%
        98%
        97%
        184 bp
        8.9%
        H14473-22_S16_L001_R1_001
        14.2%
        47%
        2.6
        H14473-22_S16_L001_R2_001
        14.0%
        47%
        2.6
        H14473-22_S16_L002_R1_001
        14.3%
        47%
        2.6
        H14473-22_S16_L002_R2_001
        13.9%
        47%
        2.6
        H14473-22_S16_L003_R1_001
        14.1%
        47%
        2.7
        H14473-22_S16_L003_R2_001
        13.9%
        47%
        2.7
        H14473-22_S16_L004_R1_001
        14.2%
        47%
        2.6
        H14473-22_S16_L004_R2_001
        13.9%
        47%
        2.6
        H14474-22
        16.8
        760
        98%
        97%
        96%
        184 bp
        9.5%
        H14474-22_S17_L001_R1_001
        13.5%
        47%
        2.4
        H14474-22_S17_L001_R2_001
        13.2%
        47%
        2.4
        H14474-22_S17_L002_R1_001
        13.4%
        47%
        2.4
        H14474-22_S17_L002_R2_001
        13.3%
        47%
        2.4
        H14474-22_S17_L003_R1_001
        13.5%
        47%
        2.5
        H14474-22_S17_L003_R2_001
        13.4%
        47%
        2.5
        H14474-22_S17_L004_R1_001
        13.7%
        47%
        2.4
        H14474-22_S17_L004_R2_001
        13.2%
        47%
        2.4
        H14475-22
        16.0
        755
        99%
        98%
        96%
        185 bp
        9.0%
        H14475-22_S18_L001_R1_001
        12.9%
        47%
        2.3
        H14475-22_S18_L001_R2_001
        12.5%
        47%
        2.3
        H14475-22_S18_L002_R1_001
        12.9%
        47%
        2.3
        H14475-22_S18_L002_R2_001
        12.4%
        47%
        2.3
        H14475-22_S18_L003_R1_001
        12.9%
        47%
        2.3
        H14475-22_S18_L003_R2_001
        12.6%
        47%
        2.3
        H14475-22_S18_L004_R1_001
        12.8%
        47%
        2.3
        H14475-22_S18_L004_R2_001
        12.3%
        47%
        2.3
        H14481-22
        15.3
        746
        99%
        98%
        95%
        185 bp
        9.6%
        H14481-22_S19_L001_R1_001
        12.6%
        47%
        2.2
        H14481-22_S19_L001_R2_001
        12.4%
        47%
        2.2
        H14481-22_S19_L002_R1_001
        12.7%
        47%
        2.2
        H14481-22_S19_L002_R2_001
        12.2%
        47%
        2.2
        H14481-22_S19_L003_R1_001
        12.8%
        47%
        2.2
        H14481-22_S19_L003_R2_001
        12.5%
        47%
        2.2
        H14481-22_S19_L004_R1_001
        12.6%
        47%
        2.2
        H14481-22_S19_L004_R2_001
        12.2%
        47%
        2.2
        H14483-22
        16.0
        802
        98%
        97%
        96%
        168 bp
        9.0%
        H14483-22_S20_L001_R1_001
        13.3%
        47%
        2.3
        H14483-22_S20_L001_R2_001
        13.2%
        47%
        2.3
        H14483-22_S20_L002_R1_001
        13.3%
        47%
        2.3
        H14483-22_S20_L002_R2_001
        13.1%
        47%
        2.3
        H14483-22_S20_L003_R1_001
        13.4%
        47%
        2.3
        H14483-22_S20_L003_R2_001
        13.3%
        47%
        2.3
        H14483-22_S20_L004_R1_001
        13.3%
        47%
        2.3
        H14483-22_S20_L004_R2_001
        13.0%
        47%
        2.3
        H14484-22
        18.9
        741
        99%
        98%
        97%
        186 bp
        9.5%
        H14484-22_S21_L001_R1_001
        14.2%
        47%
        2.7
        H14484-22_S21_L001_R2_001
        14.0%
        47%
        2.7
        H14484-22_S21_L002_R1_001
        14.3%
        47%
        2.7
        H14484-22_S21_L002_R2_001
        14.0%
        47%
        2.7
        H14484-22_S21_L003_R1_001
        14.4%
        47%
        2.8
        H14484-22_S21_L003_R2_001
        14.1%
        47%
        2.8
        H14484-22_S21_L004_R1_001
        14.1%
        47%
        2.7
        H14484-22_S21_L004_R2_001
        13.9%
        47%
        2.7
        H14485-22
        17.5
        757
        99%
        98%
        96%
        187 bp
        9.3%
        H14485-22_S22_L001_R1_001
        14.0%
        47%
        2.5
        H14485-22_S22_L001_R2_001
        13.5%
        47%
        2.5
        H14485-22_S22_L002_R1_001
        13.9%
        47%
        2.5
        H14485-22_S22_L002_R2_001
        13.4%
        47%
        2.5
        H14485-22_S22_L003_R1_001
        13.9%
        47%
        2.5
        H14485-22_S22_L003_R2_001
        13.5%
        47%
        2.5
        H14485-22_S22_L004_R1_001
        13.9%
        47%
        2.5
        H14485-22_S22_L004_R2_001
        13.6%
        47%
        2.5
        H14486-22
        19.6
        766
        99%
        98%
        97%
        184 bp
        9.5%
        H14486-22_S23_L001_R1_001
        14.8%
        47%
        2.8
        H14486-22_S23_L001_R2_001
        14.4%
        47%
        2.8
        H14486-22_S23_L002_R1_001
        14.9%
        47%
        2.8
        H14486-22_S23_L002_R2_001
        14.4%
        47%
        2.8
        H14486-22_S23_L003_R1_001
        14.8%
        47%
        2.9
        H14486-22_S23_L003_R2_001
        14.6%
        47%
        2.9
        H14486-22_S23_L004_R1_001
        15.0%
        47%
        2.8
        H14486-22_S23_L004_R2_001
        14.2%
        48%
        2.8
        H14487-22
        17.4
        757
        98%
        97%
        96%
        184 bp
        9.3%
        H14487-22_S24_L001_R1_001
        13.6%
        47%
        2.5
        H14487-22_S24_L001_R2_001
        13.2%
        47%
        2.5
        H14487-22_S24_L002_R1_001
        13.6%
        47%
        2.5
        H14487-22_S24_L002_R2_001
        13.1%
        47%
        2.5
        H14487-22_S24_L003_R1_001
        13.5%
        47%
        2.5
        H14487-22_S24_L003_R2_001
        13.3%
        47%
        2.5
        H14487-22_S24_L004_R1_001
        13.4%
        47%
        2.5
        H14487-22_S24_L004_R2_001
        13.0%
        47%
        2.5
        H14488-22
        17.6
        797
        99%
        98%
        97%
        176 bp
        9.7%
        H14488-22_S25_L001_R1_001
        14.8%
        47%
        2.5
        H14488-22_S25_L001_R2_001
        14.5%
        47%
        2.5
        H14488-22_S25_L002_R1_001
        14.7%
        47%
        2.5
        H14488-22_S25_L002_R2_001
        14.4%
        47%
        2.5
        H14488-22_S25_L003_R1_001
        14.9%
        47%
        2.6
        H14488-22_S25_L003_R2_001
        14.6%
        47%
        2.6
        H14488-22_S25_L004_R1_001
        14.8%
        47%
        2.5
        H14488-22_S25_L004_R2_001
        14.3%
        47%
        2.5
        H14494-22
        18.3
        798
        98%
        98%
        97%
        177 bp
        9.9%
        H14494-22_S26_L001_R1_001
        15.0%
        48%
        2.6
        H14494-22_S26_L001_R2_001
        14.6%
        48%
        2.6
        H14494-22_S26_L002_R1_001
        14.8%
        48%
        2.6
        H14494-22_S26_L002_R2_001
        14.4%
        48%
        2.6
        H14494-22_S26_L003_R1_001
        14.8%
        48%
        2.7
        H14494-22_S26_L003_R2_001
        14.5%
        48%
        2.7
        H14494-22_S26_L004_R1_001
        14.7%
        48%
        2.6
        H14494-22_S26_L004_R2_001
        14.3%
        48%
        2.6
        H14495-22
        19.9
        836
        98%
        98%
        97%
        170 bp
        8.4%
        H14495-22_S27_L001_R1_001
        16.1%
        48%
        2.8
        H14495-22_S27_L001_R2_001
        15.5%
        48%
        2.8
        H14495-22_S27_L002_R1_001
        16.1%
        48%
        2.8
        H14495-22_S27_L002_R2_001
        15.5%
        48%
        2.8
        H14495-22_S27_L003_R1_001
        16.1%
        48%
        2.9
        H14495-22_S27_L003_R2_001
        15.6%
        48%
        2.9
        H14495-22_S27_L004_R1_001
        16.1%
        48%
        2.8
        H14495-22_S27_L004_R2_001
        15.5%
        48%
        2.8
        H14496-22
        19.3
        813
        98%
        98%
        97%
        171 bp
        8.5%
        H14496-22_S28_L001_R1_001
        15.0%
        48%
        2.7
        H14496-22_S28_L001_R2_001
        14.7%
        48%
        2.7
        H14496-22_S28_L002_R1_001
        15.1%
        48%
        2.7
        H14496-22_S28_L002_R2_001
        14.8%
        48%
        2.7
        H14496-22_S28_L003_R1_001
        15.2%
        48%
        2.8
        H14496-22_S28_L003_R2_001
        14.9%
        48%
        2.8
        H14496-22_S28_L004_R1_001
        15.1%
        48%
        2.7
        H14496-22_S28_L004_R2_001
        14.8%
        48%
        2.7
        H14498-22
        17.7
        784
        99%
        99%
        97%
        179 bp
        11.3%
        H14498-22_S29_L001_R1_001
        14.9%
        47%
        2.6
        H14498-22_S29_L001_R2_001
        14.4%
        47%
        2.6
        H14498-22_S29_L002_R1_001
        14.8%
        47%
        2.6
        H14498-22_S29_L002_R2_001
        14.3%
        47%
        2.6
        H14498-22_S29_L003_R1_001
        14.9%
        47%
        2.6
        H14498-22_S29_L003_R2_001
        14.6%
        47%
        2.6
        H14498-22_S29_L004_R1_001
        14.9%
        47%
        2.6
        H14498-22_S29_L004_R2_001
        14.5%
        47%
        2.6
        H14499-22
        18.2
        801
        99%
        98%
        97%
        176 bp
        10.0%
        H14499-22_S30_L001_R1_001
        15.2%
        48%
        2.6
        H14499-22_S30_L001_R2_001
        14.8%
        48%
        2.6
        H14499-22_S30_L002_R1_001
        15.2%
        48%
        2.6
        H14499-22_S30_L002_R2_001
        14.7%
        48%
        2.6
        H14499-22_S30_L003_R1_001
        15.1%
        48%
        2.7
        H14499-22_S30_L003_R2_001
        14.8%
        48%
        2.7
        H14499-22_S30_L004_R1_001
        15.0%
        48%
        2.6
        H14499-22_S30_L004_R2_001
        14.9%
        48%
        2.6
        H14500-22
        18.6
        790
        99%
        98%
        97%
        178 bp
        9.6%
        H14500-22_S31_L001_R1_001
        14.9%
        47%
        2.7
        H14500-22_S31_L001_R2_001
        14.7%
        48%
        2.7
        H14500-22_S31_L002_R1_001
        15.0%
        47%
        2.7
        H14500-22_S31_L002_R2_001
        14.4%
        48%
        2.7
        H14500-22_S31_L003_R1_001
        15.1%
        47%
        2.7
        H14500-22_S31_L003_R2_001
        14.6%
        48%
        2.7
        H14500-22_S31_L004_R1_001
        14.8%
        47%
        2.7
        H14500-22_S31_L004_R2_001
        14.5%
        48%
        2.7
        H14503-22
        20.0
        778
        99%
        98%
        97%
        179 bp
        9.7%
        H14503-22_S32_L001_R1_001
        15.3%
        47%
        2.9
        H14503-22_S32_L001_R2_001
        14.8%
        48%
        2.9
        H14503-22_S32_L002_R1_001
        15.3%
        47%
        2.9
        H14503-22_S32_L002_R2_001
        15.0%
        48%
        2.9
        H14503-22_S32_L003_R1_001
        15.6%
        47%
        2.9
        H14503-22_S32_L003_R2_001
        14.9%
        47%
        2.9
        H14503-22_S32_L004_R1_001
        15.2%
        47%
        2.9
        H14503-22_S32_L004_R2_001
        14.8%
        48%
        2.9
        H14504-22
        17.5
        768
        99%
        98%
        97%
        171 bp
        15.4%
        H14504-22_S33_L001_R1_001
        15.4%
        47%
        2.7
        H14504-22_S33_L001_R2_001
        14.9%
        47%
        2.7
        H14504-22_S33_L002_R1_001
        15.6%
        47%
        2.7
        H14504-22_S33_L002_R2_001
        15.0%
        47%
        2.7
        H14504-22_S33_L003_R1_001
        15.5%
        47%
        2.7
        H14504-22_S33_L003_R2_001
        15.1%
        47%
        2.7
        H14504-22_S33_L004_R1_001
        15.3%
        47%
        2.7
        H14504-22_S33_L004_R2_001
        14.9%
        47%
        2.7
        H14505-22
        20.5
        779
        99%
        98%
        98%
        178 bp
        10.7%
        H14505-22_S34_L001_R1_001
        16.1%
        47%
        3.0
        H14505-22_S34_L001_R2_001
        15.5%
        47%
        3.0
        H14505-22_S34_L002_R1_001
        16.2%
        47%
        3.0
        H14505-22_S34_L002_R2_001
        15.3%
        47%
        3.0
        H14505-22_S34_L003_R1_001
        16.4%
        47%
        3.0
        H14505-22_S34_L003_R2_001
        15.5%
        47%
        3.0
        H14505-22_S34_L004_R1_001
        16.2%
        47%
        3.0
        H14505-22_S34_L004_R2_001
        15.3%
        47%
        3.0
        H14524-22
        20.6
        778
        98%
        97%
        97%
        176 bp
        10.8%
        H14524-22_S35_L001_R1_001
        16.1%
        47%
        3.0
        H14524-22_S35_L001_R2_001
        15.8%
        47%
        3.0
        H14524-22_S35_L002_R1_001
        16.0%
        47%
        3.0
        H14524-22_S35_L002_R2_001
        15.8%
        47%
        3.0
        H14524-22_S35_L003_R1_001
        16.3%
        47%
        3.1
        H14524-22_S35_L003_R2_001
        16.0%
        47%
        3.1
        H14524-22_S35_L004_R1_001
        16.3%
        47%
        3.0
        H14524-22_S35_L004_R2_001
        15.9%
        47%
        3.0
        H14528-22
        17.6
        793
        98%
        98%
        97%
        170 bp
        10.2%
        H14528-22_S36_L001_R1_001
        14.5%
        47%
        2.6
        H14528-22_S36_L001_R2_001
        14.1%
        47%
        2.6
        H14528-22_S36_L002_R1_001
        14.4%
        47%
        2.5
        H14528-22_S36_L002_R2_001
        13.8%
        47%
        2.5
        H14528-22_S36_L003_R1_001
        14.4%
        47%
        2.6
        H14528-22_S36_L003_R2_001
        14.1%
        47%
        2.6
        H14528-22_S36_L004_R1_001
        14.4%
        47%
        2.5
        H14528-22_S36_L004_R2_001
        13.9%
        47%
        2.5
        H14661-22
        21.4
        775
        99%
        98%
        98%
        177 bp
        11.0%
        H14661-22_S37_L001_R1_001
        16.3%
        47%
        3.1
        H14661-22_S37_L001_R2_001
        15.7%
        47%
        3.1
        H14661-22_S37_L002_R1_001
        16.2%
        47%
        3.1
        H14661-22_S37_L002_R2_001
        15.6%
        47%
        3.1
        H14661-22_S37_L003_R1_001
        16.4%
        47%
        3.2
        H14661-22_S37_L003_R2_001
        15.9%
        47%
        3.2
        H14661-22_S37_L004_R1_001
        16.2%
        47%
        3.1
        H14661-22_S37_L004_R2_001
        15.7%
        47%
        3.1
        H14683-22
        19.7
        780
        99%
        98%
        97%
        176 bp
        11.1%
        H14683-22_S38_L001_R1_001
        16.1%
        47%
        2.9
        H14683-22_S38_L001_R2_001
        15.6%
        47%
        2.9
        H14683-22_S38_L002_R1_001
        15.9%
        47%
        2.9
        H14683-22_S38_L002_R2_001
        15.5%
        47%
        2.9
        H14683-22_S38_L003_R1_001
        16.0%
        47%
        2.9
        H14683-22_S38_L003_R2_001
        15.7%
        47%
        2.9
        H14683-22_S38_L004_R1_001
        15.8%
        47%
        2.9
        H14683-22_S38_L004_R2_001
        15.5%
        47%
        2.9
        H14684-22
        20.1
        768
        99%
        98%
        97%
        176 bp
        10.5%
        H14684-22_S39_L001_R1_001
        15.2%
        47%
        2.9
        H14684-22_S39_L001_R2_001
        14.9%
        47%
        2.9
        H14684-22_S39_L002_R1_001
        15.4%
        47%
        2.9
        H14684-22_S39_L002_R2_001
        15.0%
        47%
        2.9
        H14684-22_S39_L003_R1_001
        15.3%
        47%
        3.0
        H14684-22_S39_L003_R2_001
        15.1%
        47%
        3.0
        H14684-22_S39_L004_R1_001
        15.1%
        47%
        2.9
        H14684-22_S39_L004_R2_001
        14.9%
        47%
        2.9
        H14686-22
        19.9
        767
        99%
        98%
        97%
        178 bp
        11.9%
        H14686-22_S40_L001_R1_001
        16.1%
        47%
        2.9
        H14686-22_S40_L001_R2_001
        15.6%
        47%
        2.9
        H14686-22_S40_L002_R1_001
        16.1%
        47%
        2.9
        H14686-22_S40_L002_R2_001
        15.6%
        47%
        2.9
        H14686-22_S40_L003_R1_001
        16.1%
        47%
        3.0
        H14686-22_S40_L003_R2_001
        15.6%
        47%
        3.0
        H14686-22_S40_L004_R1_001
        16.1%
        47%
        2.9
        H14686-22_S40_L004_R2_001
        15.5%
        47%
        2.9
        H14687-22
        18.5
        807
        98%
        98%
        97%
        175 bp
        10.5%
        H14687-22_S41_L001_R1_001
        15.5%
        47%
        2.7
        H14687-22_S41_L001_R2_001
        15.0%
        48%
        2.7
        H14687-22_S41_L002_R1_001
        15.4%
        47%
        2.7
        H14687-22_S41_L002_R2_001
        14.9%
        48%
        2.7
        H14687-22_S41_L003_R1_001
        15.5%
        47%
        2.7
        H14687-22_S41_L003_R2_001
        15.1%
        47%
        2.7
        H14687-22_S41_L004_R1_001
        15.4%
        47%
        2.7
        H14687-22_S41_L004_R2_001
        14.9%
        48%
        2.7
        H14688-22
        20.2
        809
        99%
        98%
        97%
        174 bp
        11.2%
        H14688-22_S42_L001_R1_001
        17.5%
        48%
        3.0
        H14688-22_S42_L001_R2_001
        16.9%
        48%
        3.0
        H14688-22_S42_L002_R1_001
        17.5%
        48%
        3.0
        H14688-22_S42_L002_R2_001
        17.1%
        48%
        3.0
        H14688-22_S42_L003_R1_001
        17.5%
        48%
        3.0
        H14688-22_S42_L003_R2_001
        17.2%
        48%
        3.0
        H14688-22_S42_L004_R1_001
        17.4%
        48%
        3.0
        H14688-22_S42_L004_R2_001
        17.0%
        48%
        3.0
        H14789-22
        20.3
        873
        98%
        97%
        97%
        152 bp
        8.9%
        H14789-22_S43_L001_R1_001
        16.6%
        48%
        2.9
        H14789-22_S43_L001_R2_001
        16.3%
        48%
        2.9
        H14789-22_S43_L002_R1_001
        16.5%
        48%
        2.9
        H14789-22_S43_L002_R2_001
        16.4%
        48%
        2.9
        H14789-22_S43_L003_R1_001
        16.8%
        48%
        3.0
        H14789-22_S43_L003_R2_001
        16.5%
        48%
        3.0
        H14789-22_S43_L004_R1_001
        16.5%
        48%
        2.9
        H14789-22_S43_L004_R2_001
        16.3%
        48%
        2.9
        H14823-22
        18.5
        802
        98%
        97%
        97%
        175 bp
        10.7%
        H14823-22_S44_L001_R1_001
        15.2%
        47%
        2.7
        H14823-22_S44_L001_R2_001
        14.9%
        47%
        2.7
        H14823-22_S44_L002_R1_001
        15.2%
        47%
        2.7
        H14823-22_S44_L002_R2_001
        14.7%
        47%
        2.7
        H14823-22_S44_L003_R1_001
        15.1%
        47%
        2.7
        H14823-22_S44_L003_R2_001
        14.8%
        47%
        2.7
        H14823-22_S44_L004_R1_001
        14.8%
        47%
        2.7
        H14823-22_S44_L004_R2_001
        14.6%
        47%
        2.7
        H14902-22
        19.3
        792
        99%
        98%
        97%
        176 bp
        10.9%
        H14902-22_S45_L001_R1_001
        16.0%
        47%
        2.8
        H14902-22_S45_L001_R2_001
        15.7%
        48%
        2.8
        H14902-22_S45_L002_R1_001
        16.2%
        47%
        2.8
        H14902-22_S45_L002_R2_001
        15.7%
        48%
        2.8
        H14902-22_S45_L003_R1_001
        16.1%
        47%
        2.9
        H14902-22_S45_L003_R2_001
        16.0%
        48%
        2.9
        H14902-22_S45_L004_R1_001
        16.1%
        47%
        2.8
        H14902-22_S45_L004_R2_001
        15.8%
        48%
        2.8
        H15020-22
        17.4
        758
        99%
        98%
        97%
        179 bp
        13.5%
        H15020-22_S46_L001_R1_001
        15.1%
        47%
        2.6
        H15020-22_S46_L001_R2_001
        14.9%
        47%
        2.6
        H15020-22_S46_L002_R1_001
        15.3%
        47%
        2.6
        H15020-22_S46_L002_R2_001
        14.9%
        47%
        2.6
        H15020-22_S46_L003_R1_001
        15.2%
        47%
        2.7
        H15020-22_S46_L003_R2_001
        14.9%
        47%
        2.7
        H15020-22_S46_L004_R1_001
        15.1%
        47%
        2.6
        H15020-22_S46_L004_R2_001
        14.8%
        47%
        2.6
        H33509-21
        19.7
        752
        98%
        98%
        97%
        187 bp
        9.5%
        H33509-21_S1_L001_R1_001
        15.0%
        47%
        2.8
        H33509-21_S1_L001_R2_001
        14.5%
        47%
        2.8
        H33509-21_S1_L002_R1_001
        15.2%
        47%
        2.8
        H33509-21_S1_L002_R2_001
        14.6%
        47%
        2.8
        H33509-21_S1_L003_R1_001
        15.1%
        47%
        2.9
        H33509-21_S1_L003_R2_001
        14.8%
        47%
        2.9
        H33509-21_S1_L004_R1_001
        15.1%
        47%
        2.8
        H33509-21_S1_L004_R2_001
        14.7%
        47%
        2.8
        H99999-21
        20.6
        850
        99%
        98%
        97%
        154 bp
        11.1%
        H99999-21_S48_L001_R1_001
        16.7%
        48%
        3.0
        H99999-21_S48_L001_R2_001
        16.5%
        48%
        3.0
        H99999-21_S48_L002_R1_001
        16.7%
        48%
        3.0
        H99999-21_S48_L002_R2_001
        16.5%
        48%
        3.0
        H99999-21_S48_L003_R1_001
        16.8%
        48%
        3.1
        H99999-21_S48_L003_R2_001
        16.7%
        48%
        3.1
        H99999-21_S48_L004_R1_001
        16.8%
        48%
        3.0
        H99999-21_S48_L004_R2_001
        16.4%
        48%
        3.0
        Undetermined
        18.9
        780
        99%
        98%
        97%
        176 bp
        7.7%
        Undetermined_S0_L001_R1_001
        9.2%
        44%
        3.4
        Undetermined_S0_L001_R2_001
        8.4%
        45%
        3.4
        Undetermined_S0_L002_R1_001
        9.7%
        44%
        3.6
        Undetermined_S0_L002_R2_001
        9.4%
        45%
        3.6
        Undetermined_S0_L003_R1_001
        9.4%
        44%
        3.5
        Undetermined_S0_L003_R2_001
        8.9%
        45%
        3.5
        Undetermined_S0_L004_R1_001
        9.3%
        44%
        3.6
        Undetermined_S0_L004_R2_001
        8.8%
        45%
        3.6

        Picard

        Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

        HSMetrics

        Showing 49/49 rows and 22/27 columns.
        Sample NameBait design efficiencyFold 80 base penaltyFold enrichmentHet snp qHet snp sensitivityM Near bait basesM Off bait basesM On bait basesM On target basesM Pf basesM Pf bases alignedM Pf readsM Pf unique readsM Pf uq bases alignedM Pf uq reads alignedMax target coverageMean bait coverageMean target coverageMedian target coverageMin target coverageOn bait vs selectedZero cvg targets pct
        H10334-22
        1.0
        1.5
        754.3
        22.0
        1.0
        271.4
        632.6
        517.2
        457.5
        1492.4
        1421.2
        20.2
        20.2
        1421.2
        19.3
        1495.0
        341.7
        302.3
        200.0
        0.0
        0.7
        0.0
        H11184-22
        1.0
        1.3
        785.1
        19.0
        1.0
        231.7
        515.8
        455.7
        401.5
        1262.7
        1203.2
        17.1
        17.1
        1203.2
        16.3
        1517.0
        301.1
        265.3
        200.0
        0.0
        0.7
        0.0
        H13025-22
        1.0
        1.5
        868.7
        20.0
        1.0
        193.0
        572.6
        552.4
        459.4
        1389.1
        1318.0
        18.8
        18.8
        1318.0
        17.9
        1168.0
        364.9
        303.6
        200.0
        0.0
        0.7
        0.0
        H13110-22
        1.0
        1.4
        880.8
        19.0
        1.0
        161.4
        515.4
        500.2
        409.0
        1246.8
        1177.0
        16.8
        16.8
        1177.0
        16.0
        1206.0
        330.5
        270.3
        200.0
        0.0
        0.8
        0.0
        H13191-22
        1.0
        1.4
        874.6
        21.0
        1.0
        146.7
        476.3
        454.8
        372.0
        1143.1
        1077.8
        15.4
        15.4
        1077.8
        14.6
        1011.0
        300.5
        245.8
        200.0
        0.0
        0.8
        0.0
        H13741-22
        1.0
        1.5
        771.1
        21.0
        1.0
        269.6
        605.8
        518.7
        458.3
        1465.2
        1394.1
        19.8
        19.8
        1394.1
        18.9
        1239.0
        342.7
        302.8
        200.0
        0.0
        0.7
        0.0
        H13764-22
        1.0
        1.5
        774.0
        18.0
        1.0
        267.6
        601.8
        518.1
        458.1
        1454.6
        1387.6
        19.7
        19.7
        1387.6
        18.8
        1555.0
        342.3
        302.7
        200.0
        0.0
        0.7
        0.0
        H13876-22
        1.0
        1.5
        778.1
        21.0
        1.0
        257.5
        582.6
        505.0
        444.3
        1421.1
        1345.1
        19.2
        19.2
        1345.1
        18.2
        1327.0
        333.6
        293.5
        200.0
        0.0
        0.7
        0.0
        H14091-22
        1.0
        1.5
        761.8
        19.0
        1.0
        256.0
        619.0
        508.5
        443.9
        1468.1
        1383.4
        19.8
        19.8
        1383.4
        18.8
        1197.0
        335.9
        293.3
        200.0
        0.0
        0.7
        0.0
        H14210-22
        1.0
        1.5
        764.7
        23.0
        1.0
        251.7
        613.8
        505.9
        442.9
        1445.6
        1371.4
        19.5
        19.5
        1371.4
        18.6
        1238.0
        334.3
        292.6
        200.0
        0.0
        0.7
        0.0
        H14328-22
        1.0
        1.5
        760.1
        19.0
        1.0
        261.6
        606.0
        502.4
        444.7
        1437.3
        1369.9
        19.4
        19.4
        1369.9
        18.6
        1275.0
        331.9
        293.8
        200.0
        0.0
        0.7
        0.0
        H14329-22
        1.0
        1.4
        747.5
        22.0
        1.0
        238.6
        567.6
        454.8
        400.4
        1328.3
        1261.1
        18.0
        18.0
        1261.1
        17.1
        1013.0
        300.5
        264.5
        200.0
        0.0
        0.7
        0.0
        H14341-22
        1.0
        1.3
        768.6
        20.0
        1.0
        211.6
        509.4
        424.9
        372.8
        1204.6
        1145.8
        16.3
        16.3
        1145.8
        15.5
        1155.0
        280.7
        246.3
        200.0
        0.0
        0.7
        0.0
        H14462-22
        1.0
        1.4
        760.9
        22.0
        1.0
        226.7
        542.6
        446.2
        391.3
        1275.9
        1215.6
        17.2
        17.2
        1215.6
        16.5
        1733.0
        294.8
        258.6
        200.0
        0.0
        0.7
        0.0
        H14466-22
        1.0
        1.4
        744.2
        24.0
        1.0
        229.6
        549.5
        436.4
        385.0
        1274.6
        1215.5
        17.2
        17.2
        1215.5
        16.5
        1075.0
        288.3
        254.4
        200.0
        0.0
        0.7
        0.0
        H14473-22
        1.0
        1.5
        771.6
        20.0
        1.0
        251.5
        600.5
        505.2
        444.2
        1426.1
        1357.1
        19.3
        19.3
        1357.1
        18.4
        1201.0
        333.8
        293.5
        200.0
        0.0
        0.7
        0.0
        H14474-22
        1.0
        1.3
        759.6
        19.0
        1.0
        228.6
        557.6
        454.9
        399.1
        1302.0
        1241.1
        17.6
        17.6
        1241.1
        16.8
        1464.0
        300.5
        263.7
        200.0
        0.0
        0.7
        0.0
        H14475-22
        1.0
        1.4
        755.0
        22.0
        1.0
        218.2
        532.8
        430.2
        376.6
        1243.6
        1181.2
        16.8
        16.8
        1181.2
        16.0
        988.0
        284.3
        248.8
        200.0
        0.0
        0.7
        0.0
        H14481-22
        1.0
        1.4
        746.3
        21.0
        1.0
        207.4
        515.3
        406.6
        357.1
        1186.4
        1129.3
        16.0
        16.0
        1129.3
        15.3
        1011.0
        268.6
        235.9
        200.0
        0.0
        0.7
        0.0
        H14483-22
        1.0
        1.3
        802.4
        19.0
        1.0
        197.6
        522.9
        455.2
        392.2
        1234.1
        1175.7
        16.7
        16.7
        1175.7
        16.0
        1049.0
        300.7
        259.1
        200.0
        0.0
        0.7
        0.0
        H14484-22
        1.0
        1.5
        741.0
        20.0
        1.0
        258.0
        639.1
        499.2
        439.8
        1463.7
        1396.3
        19.8
        19.8
        1396.3
        18.9
        1260.0
        329.8
        290.6
        200.0
        0.0
        0.7
        0.0
        H14485-22
        1.0
        1.4
        757.0
        23.0
        1.0
        242.1
        576.1
        470.8
        414.4
        1355.0
        1289.0
        18.3
        18.3
        1289.0
        17.5
        1425.0
        311.0
        273.8
        200.0
        0.0
        0.7
        0.0
        H14486-22
        1.0
        1.6
        766.3
        20.0
        1.0
        267.4
        645.8
        535.6
        470.2
        1523.6
        1448.8
        20.6
        20.6
        1448.8
        19.6
        1604.0
        353.9
        310.6
        200.0
        0.0
        0.7
        0.0
        H14487-22
        1.0
        1.4
        756.7
        19.0
        1.0
        236.1
        579.7
        469.1
        411.9
        1351.8
        1284.9
        18.3
        18.3
        1284.9
        17.4
        1270.0
        309.9
        272.1
        200.0
        0.0
        0.7
        0.0
        H14488-22
        1.0
        1.4
        797.3
        22.0
        1.0
        232.8
        567.0
        499.9
        434.0
        1364.3
        1299.7
        18.4
        18.4
        1299.7
        17.6
        1242.0
        330.3
        286.8
        200.0
        0.0
        0.7
        0.0
        H14494-22
        1.0
        1.5
        797.7
        19.0
        1.0
        241.2
        589.8
        519.9
        452.9
        1418.6
        1350.8
        19.2
        19.2
        1350.8
        18.3
        1303.0
        343.5
        299.2
        200.0
        0.0
        0.7
        0.0
        H14495-22
        1.0
        1.7
        835.6
        19.0
        1.0
        256.4
        619.4
        591.6
        511.6
        1545.7
        1467.5
        20.9
        20.9
        1467.5
        19.9
        1516.0
        390.9
        338.0
        200.0
        0.0
        0.7
        0.0
        H14496-22
        1.0
        1.6
        813.4
        19.0
        1.0
        246.1
        618.2
        558.2
        483.4
        1492.4
        1422.5
        20.2
        20.2
        1422.5
        19.3
        2054.0
        368.8
        319.4
        200.0
        0.0
        0.7
        0.0
        H14498-22
        1.0
        1.4
        784.2
        24.0
        1.0
        236.5
        574.6
        493.6
        429.3
        1368.8
        1304.8
        18.5
        18.5
        1304.8
        17.7
        1123.0
        326.2
        283.6
        200.0
        0.0
        0.7
        0.0
        H14499-22
        1.0
        1.5
        801.1
        22.0
        1.0
        241.9
        581.4
        518.7
        451.2
        1405.5
        1342.0
        19.0
        19.0
        1342.0
        18.2
        1325.0
        342.7
        298.1
        200.0
        0.0
        0.7
        0.0
        H14500-22
        1.0
        1.5
        790.4
        22.0
        1.0
        249.0
        601.3
        524.1
        456.7
        1443.1
        1374.4
        19.5
        19.5
        1374.4
        18.6
        1752.0
        346.3
        301.7
        200.0
        0.0
        0.7
        0.0
        H14503-22
        1.0
        1.6
        777.6
        22.0
        1.0
        266.6
        653.4
        552.4
        482.8
        1548.1
        1472.5
        20.9
        20.9
        1472.5
        20.0
        1490.0
        365.0
        319.0
        200.0
        0.0
        0.7
        0.0
        H14504-22
        1.0
        1.4
        767.6
        23.0
        1.0
        216.3
        594.2
        476.8
        410.1
        1362.3
        1287.3
        18.4
        18.4
        1287.3
        17.5
        1219.0
        315.0
        271.0
        200.0
        0.0
        0.7
        0.0
        H14505-22
        1.0
        1.6
        779.4
        23.0
        1.0
        271.7
        672.3
        568.9
        494.0
        1594.4
        1512.8
        21.5
        21.5
        1512.8
        20.5
        1482.0
        375.8
        326.4
        200.0
        0.0
        0.7
        0.0
        H14524-22
        1.0
        1.6
        777.6
        19.0
        1.0
        268.8
        681.6
        570.6
        496.7
        1598.3
        1521.0
        21.6
        21.6
        1521.0
        20.6
        1741.0
        377.0
        328.2
        200.0
        0.0
        0.7
        0.0
        H14528-22
        1.0
        1.4
        793.2
        18.0
        1.0
        220.2
        582.4
        497.5
        429.7
        1367.0
        1300.2
        18.5
        18.5
        1300.2
        17.6
        1340.0
        328.7
        283.9
        200.0
        0.0
        0.7
        0.0
        H14661-22
        1.0
        1.7
        774.5
        23.0
        1.0
        278.6
        709.3
        589.4
        510.7
        1662.3
        1577.3
        22.5
        22.5
        1577.3
        21.4
        1252.0
        389.4
        337.4
        200.0
        0.0
        0.7
        0.0
        H14683-22
        1.0
        1.6
        779.9
        21.0
        1.0
        257.9
        646.4
        545.5
        475.0
        1522.9
        1449.7
        20.6
        20.6
        1449.7
        19.7
        1647.0
        360.4
        313.8
        200.0
        0.0
        0.7
        0.0
        H14684-22
        1.0
        1.6
        768.4
        22.0
        1.0
        258.3
        672.7
        548.5
        478.0
        1551.6
        1479.5
        21.0
        21.0
        1479.5
        20.1
        1367.0
        362.4
        315.8
        200.0
        0.0
        0.7
        0.0
        H14686-22
        1.0
        1.6
        767.3
        23.0
        1.0
        259.8
        663.5
        542.6
        472.6
        1542.2
        1465.8
        20.8
        20.8
        1465.8
        19.9
        1847.0
        358.5
        312.3
        200.0
        0.0
        0.7
        0.0
        H14687-22
        1.0
        1.5
        806.8
        19.0
        1.0
        243.7
        590.8
        531.8
        461.7
        1433.0
        1366.4
        19.4
        19.4
        1366.4
        18.5
        1679.0
        351.4
        305.0
        200.0
        0.0
        0.7
        0.0
        H14688-22
        1.0
        1.7
        808.8
        20.0
        1.0
        263.5
        645.5
        581.7
        503.1
        1569.5
        1490.7
        21.2
        21.2
        1490.7
        20.2
        1526.0
        384.3
        332.4
        200.0
        0.0
        0.7
        0.0
        H14789-22
        1.0
        1.7
        873.3
        19.0
        1.0
        226.9
        636.3
        628.5
        529.4
        1580.6
        1491.7
        21.4
        21.4
        1491.7
        20.3
        1567.0
        415.2
        349.8
        200.0
        0.0
        0.7
        0.0
        H14823-22
        1.0
        1.5
        801.5
        18.0
        1.0
        242.5
        592.2
        526.3
        457.0
        1431.2
        1361.0
        19.3
        19.3
        1361.0
        18.5
        1269.0
        347.7
        302.0
        200.0
        0.0
        0.7
        0.0
        H14902-22
        1.0
        1.6
        791.9
        22.0
        1.0
        252.8
        627.2
        544.1
        473.2
        1496.3
        1424.0
        20.2
        20.2
        1424.0
        19.3
        1513.0
        359.5
        312.6
        200.0
        0.0
        0.7
        0.0
        H15020-22
        1.0
        1.4
        757.5
        20.0
        1.0
        229.0
        585.3
        469.0
        409.3
        1351.1
        1283.3
        18.3
        18.3
        1283.3
        17.4
        1210.0
        309.9
        270.5
        200.0
        0.0
        0.7
        0.0
        H33509-21
        1.0
        1.5
        751.5
        20.0
        1.0
        274.2
        653.4
        527.6
        466.0
        1536.1
        1455.2
        20.8
        20.8
        1455.2
        19.7
        1540.0
        348.6
        307.9
        200.0
        0.0
        0.7
        0.0
        H99999-21
        1.0
        1.7
        850.3
        24.0
        1.0
        231.8
        663.1
        622.5
        523.5
        1598.3
        1517.4
        21.6
        21.6
        1517.4
        20.6
        1410.0
        411.3
        345.9
        200.0
        0.0
        0.7
        0.0
        Undetermined
        1.0
        1.5
        780.2
        25.0
        1.0
        244.3
        622.2
        523.1
        444.5
        1963.6
        1389.7
        26.5
        26.5
        1389.7
        18.9
        2640.0
        345.6
        293.7
        200.0
        0.0
        0.7
        0.0

        Target Region Coverage

        The percentage of all target bases with at least x fold coverage.

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        Insert Size

        Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

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        Mark Duplicates

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        Samtools

        Samtools is a suite of programs for interacting with high-throughput sequencing data.

        Samtools Flagstat

        This module parses the output from samtools flagstat. All numbers in millions.

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        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Length Distribution

        All samples have sequences of a single length (74bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        392 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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        MultiQC v1.8 (4c6300c) - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.